Publications

phage genomics: small is beautiful.	the age of genomics dawned only gradually for bacteriophages. it was 1977 when the genome of phage phi x174 was published and 1983 when the "large" genome of phage lambda hit the streets. more recently, the pace has quickened, so that we now have over 100 complete phage genomes and can expect thousands in a very few years. these sequences have been marvelously informative for the biology of the individual phages, but with the advent of high volume sequencing technology, the real excitement for p ...	2002	11792317
simultaneous topographic and fluorescence imaging of single dna molecules for dna analysis with a scanning near-field optical/atomic force microscope.	high-resolution fluorescence imaging of lambda-phage dna molecules, intercalated with the dye yoyo-1, has been performed by a snom/afm based on a bent-type optical fiber probe. a modified design of the optical probe has been made, and successful near-field optical resolution has been obtained for the strongly stretched lambda-phage dna molecules. the best optical resolution was estimated at 45 nm for the dye-intercalated single lambda-dna molecules by a mean width evaluation. in our comparison b ...	2001	11791570
inhibition of bacteriophage lambda protein phosphatase by organic and oxoanion inhibitors.	bacteriophage lambda protein phosphatase (lambdapp) with mn(2+) as the activating metal cofactor was studied using phosphatase inhibition kinetics and electron paramagnetic resonance (epr) spectroscopy. orthophosphate and the oxoanion analogues orthovanadate, tungstate, molybdate, arsenate, and sulfate were shown to inhibit the phosphomonoesterase activity of lambdapp, albeit with inhibition constants (k(i)) that range over 5 orders of magnitude. in addition, small organic anions were tested as ...	2002	11790129
structure and expression of the mouse cardiac calsequestrin gene.	calsequestrin is a sarcoplasmic reticulum protein, which plays a predominant role in diastolic ca2+-storage in the mammalian heart. the present study was designed to define the gene structure, developmental and tissue specific expression of the murine, cardiac isoform of calsequestrin. two sets of genomic libraries (lambda phage and pac) were screened using the mouse cardiac calsequestrin cdna, and several overlapping clones were isolated. these clones were characterized using restriction enzyme ...	2001	11770083
mutational changes of conserved residues in the q-loop region of transcription factor rho greatly reduce secondary site rna-binding.	transcription factor rho of eschericia coli is a ring-shaped homohexameric protein that terminates transcripts by its action on nascent rnas. to test the functional importance of the phylogenetically highly conserved residues of the q-loop region, four mutant rho proteins, s281a, k283a, t286a and d290a, were isolated and analyzed for their biochemical properties. all four proteins were very defective in terminating transcripts in vitro at the bacteriophage lambda tr1 terminator and had correspon ...	2001	11743718
epitope tagging of chromosomal genes in salmonella.	we have developed a simple and efficient procedure for adding an epitope-encoding tail to one or more genes of interest in the bacterial chromosome. the procedure is a modification of the gene replacement method of datsenko and wanner [datsenko, k. a. & wanner, b. l. (2000) proc. natl. acad. sci. usa 97, 6640-6645]. a dna module that begins with the epitope-encoding sequence and includes a selectable marker is amplified by pcr with primers that carry extensions (as short as 36 nt) homologous to ...	2001	11742086
amplified uvra protein can ameliorate the ultraviolet sensitivity of an escherichia coli reca mutant.	when a reca strain of escherichia coli was transformed with the multicopy plasmid psf11 carrying the uvra gene of e. coli, its extreme ultraviolet (uv) sensitivity was decreased. the sensitivity of the lexa1 (ind(-)) strain to uv was also decreased by psf11. the reca cells expressing neurospora crassa uv damage endonuclease (uvde), encoding uv-endonuclease, show uv resistance. on the other hand, only partial amelioration of uv sensitivity of the reca strain was observed in the presence of the pl ...	2001	11738941
cryoelectron microscopy of lambda phage dna condensates in vitreous ice: the fine structure of dna toroids.	dna toroids produced by the condensation of lambda phage dna with hexammine cobalt (iii) have been investigated by cryoelectron microscopy. image resolution obtained by this technique has allowed unprecedented views of dna packing within toroidal condensates. toroids oriented coplanar with the microscope image plane exhibit circular fringes with a repeat spacing of 2.4 nm. for some toroids these fringes are observed around almost the entire circumference of the toroid. however, for most toroids ...	2001	11734630
role of serex-defined immunogenic wild-type cellular molecules in the development of tumor-specific immunity.	recognition of altered self-antigens in tumor cells by lymphocytes forms the basis for antitumor immune responses. the effector cells in most experimental tumor systems are cd8(+) t cells that recognize mhc class i binding peptides derived from molecules with altered expression in tumor cells. although the need for cd4(+) helper t cells in regulating cd8(+) t cells has been documented, their target epitopes and functional impact in antitumor responses remain unclear. we examined whether broadly ...	2001	11724951
control of intrinsic transcription termination by n and nusa: the basic mechanisms.	intrinsic transcription termination plays a crucial role in regulating gene expression in prokaryotes. after a short pause, the termination signal appears in rna as a hairpin that destabilizes the elongation complex (ec). we demonstrate that negative and positive termination factors control the efficiency of termination primarily through a direct modulation of hairpin folding and, to a much lesser extent, by changing pausing at the point of termination. the mechanism controlling hairpin formatio ...	2001	11719185
the bacteriophage lambda dna packaging enzyme: identification of four structural domains of the gpnu1 subunit using limited proteolysis.	lambda dna terminase, the enzyme that cleaves virion-length chromosomes from multigenomic concatemers and packages them into the bacteriophage head, is composed of two subunits, gpnu1 and gpa. direct determination of the structure of gpnu1, the smaller subunit, has not been possible because of its insolubility in aqueous solutions. therefore, to identify smaller and potentially water-soluble domains of gpnu1, we analyzed the nature of the products obtained by limited digestion of the protein wit ...	2001	11715858
behavior of dna fibers stretched by precise meniscus motion control.	a modified dna combing method, which can precisely locate straightened dna fibers on a substrate, has been developed. precise motion control of a dna solution droplet on hydrophobic surfaces has allowed detailed analyses of dna straightening behavior. our method provides a technique for consistently straightening lambda phage dna on a trace of droplet motion, though the straightened dnas had several variations in their alignments. the dependence of the straightened dna frequency upon motion rate ...	2001	11713329
octamerization of lambda ci repressor is needed for effective repression of p(rm) and efficient switching from lysogeny.	the ci repressor of bacteriophage lambda is a model for the role of cooperativity in the efficient functioning of genetic switches. pairs of ci dimers interact to cooperatively occupy adjacent operator sites at o(r) and at o(l). these ci tetramers repress the lytic promoters and activate transcription of the ci gene from p(rm). ci is also able to octamerize, forming a large dna loop between o(r) and o(l), but the physiological role of this is unclear. another puzzle is that, although a dimer of ...	2001	11711436
foreign dna integration--perturbations of the genome--oncogenesis.	we have been interested in the consequences of foreign dna insertion into established mammalian genomes and have initially studied this problem in adenovirus type 12 (ad12)-transformed cells or in ad12-induced hamster tumors. since integrates are frequently methylated de novo, it appears that they might be modified by an ancient defense mechanism against foreign dna. in cells transgenic for the dna of ad12 or for the dna of bacteriophage lambda, changes in cellular methylation and transcription ...	2001	11708490
the helix-turn-helix motif of the coliphage 186 immunity repressor binds to two distinct recognition sequences.	the ci protein of coliphage 186 is responsible for maintaining the stable lysogenic state. to do this ci must recognize two distinct dna sequences, termed a type sites and b type sites. here we investigate whether ci contains two separate dna binding motifs or whether ci has one motif that recognizes two different operator sequences. sequence alignment with 186-like repressors predicts an n-terminal helix-turn-helix (hth) motif, albeit with poor homology to a large master set of such motifs. the ...	2002	11700308
tumor antigens isolated from a patient with vitiligo and t-cell-infiltrated melanoma.	serological identification of tumor antigens by cdna expression cloning is a technique used to isolate cdnas encoding tumor antigens that are recognized by igg antibodies in sera from cancer patients. it is also useful for the isolation of tumor antigens recognized by t cells. we applied this method to identify melanoma antigens recognized by the serum from a patient with a good prognosis who had t-cell-infiltrated melanoma and vitiligo. by screening a lambda phage cdna library constructed from ...	2001	11691810
purification and crystallization of cii: an unstable transcription activator from phage lambda.	the cii protein of the temperate bacteriophage lambda is a transcriptional activator involved in the lysis-lysogeny switch of the phage. it is an unstable protein of 97 amino acids and is known to exist as a tetramer in the native state. the cii gene has been cloned and expressed in escherichia coli using a t7 promoter based over-expression system. the recombinant cii protein has been purified to homogeneity by ammonium sulfate fractionation followed by two steps of ion-exchange chromatography. ...	2001	11689008
the functional asymmetry of cosn, the nicking site for bacteriophage lambda dna packaging, is dependent on the terminase binding site, cosb.	cosn is the site at which terminase, the dna packaging enzyme of phage lambda, introduces staggered nicks into viral concatemeric dna to initiate genome packaging. although the nick positions and many of the base pairs of cosn show 2-fold rotational symmetry, cosn is functionally asymmetric. that is, the cosn g2c mutation in the left half-site (cosnl) causes a strong virus growth defect whereas the symmetrically disposed cosn c11g mutation in the right half-site (cosnr) does not affect virus gro ...	2001	11683647
elucidation of solvent exposure, side-chain reactivity, and steric demands of the trifluoromethionine residue in a recombinant protein.	when incorporated into proteins, fluorinated amino acids have been utilized as 19f nmr probes of protein structure and protein-ligand interactions, and as subtle structural replacements for their parent amino acids which is not possible using the standard 20-amino acid repertoire. recent investigations have shown the ability of various fluorinated methionines, such as difluoromethionine (dfm) and trifluoromethionine (tfm), to be bioincorporated into recombinant proteins and to be extremely usefu ...	2001	11683625
inhibitory effects of gynostemma pentaphyllum on the uv induction of bacteriophage lambda in lysogenic escherichia coli.	effects of gynostemma pentaphyllum (gp) on the bacteriophage lambda induced by ultraviolet (uv) irradiation have been studied. the results showed that gp could inhibit the uv induction of bacteriophage lambda in lysogenic cells. the inhibitory effects were dependent on the concentration and the reaction time of gp, and were efficient at 40 to approximately 125 microg ml(-1) for 10 min. the inhibitory rate was higher than 70% when the gp concentration was 50 microg ml(-1). by electron spin resona ...	2001	11683367
calf thymus hsc70 and hsc40 can substitute for dnak and dnaj function in protein renaturation but not in bacteriophage dna replication.	calf thymus (ct) hsc70 has been shown previously to reactivate heat-inactivated prokaryotic and eukaryotic enzymes, while dnak was able to reactivate solely prokaryotic enzymes. here, we report on isolation from calf thymus of a dnaj homolog, cthsc40, and on testing of its cooperative function in three different assays: (i) reactivation of heat-inactivated dna polymerases, (ii) stimulation of the atpase activity of cthsc70 chaperone, and (iii) replication of bacteriophage lambda dna. surprisingl ...	2001	11682050
the bacteriophage lambda attachment site in wild strains of escherichia coli.	the attachment site (attlambda) of bacteriophage lambda was examined in wild strains of escherichia coli. although the att region is non-coding, the dna sequence was invariant in the 13 strains examined. two other non-coding regions showed nine changes, all associated with a single strain. in four of 33 strains, sequences were inserted in or near the attlambda site and in two of these the insert was related to lambda. among strains that can be lysogenized by lambda, integration was via the attla ...	2001	11677620
rapid degradation of bacteriophage lambda o protein by clpp/clpx protease influences the lysis-versus-lysogenization decision of the phage under certain growth conditions of the host cells.	the initiator of bacteriophage lambda dna replication, the o protein, is rapidly degraded in escherichia coli by the clpp/clpx protease encoded by the host. although the biochemical mechanism of this degradation has been investigated intensively, a physiological role for this process remained unknown since little effect of dysfunction of clpp and clpx genes on the lytic development of the phage was observed. here we demonstrate that activities of clpp and clpx genes influence the lysis-versus-ly ...	2001	11676412
the dirs1 group of retrotransposons.	only three retrotransposons of the dirs1 group have previously been described: dirs1 from the slime mold dictyostelium discoideum, pat from the nematode panagrellus redivivus, and prt1 from the zygomycetous fungus phycomyces blakesleeanus. analyses of the reverse transcriptase sequences encoded by these elements suggest that they are related to the long terminal repeat (ltr) retroelements, such as the ty3/gypsy retrotransposons and the vertebrate retroviruses. the dirs1-group elements, however, ...	2001	11606703
[formation of recognition site in transcription factors: repressor of phage lambda and a murine immunoglobulin factor].	ipolar interactions between protein and the major groove of double-stranded dna have been analyzed on the basis of a structural study of the complexes formed by two transcription factors: phage lambda repressor and murine immunoglobulin transcription factor nf kappa b-p50. two identical molecules of these two factors form two binding sites within two different parts of a single dna molecule. this allows one to study formation of the recognition module by comparing the binding pattern of two diff ...	2001	11605537
genetic selection for and molecular dynamic modeling of a protein transmembrane domain multimerization motif from a random escherichia coli genomic library.	in order to identify new transmembrane helix packing motifs in naturally occurring proteins, we have selected transmembrane domains from a library of random escherichia coli genomic dna fragments and screened them for homomultimerization via their abilities to dimerize the bacteriophage lambda ci repressor dna-binding domain. sequences were isolated using a modified lambda ci headpiece dimerization assay system, which was shown previously to measure transmembrane helix-helix association in the e ...	2001	11601855
genomic organization of the human thyroglobulin gene: the complete intron-exon structure.	in order to complete the knowledge of the genomic organization of the human thyroglobulin gene, the present work was designed to establish the intron-exon organization from exon 24 to exon 35 and to construct a more complete physical map of the gene.	2001	11581009
numerical comparison of several approximations of the word count distribution in random sequences.	the exact distribution of word counts in random sequences and several approximations have been proposed in the past few years. the exact distribution has no theoretical limit but may require prohibitive computation time. on the other hand, approximate distributions can be rapidly calculated but, in practice, are only accurate under specific conditions. after making a survey of these distributions, we compare them according to both their accuracy and computational cost. rules are suggested for ch ...	2001	11571071
microfabricated polycarbonate ce devices for dna analysis.	the microchip capillary electrophoresis (ce) devices were fabricated in polycarbonate (pc) plastic material by compression molding. the molded devices were enclosed utilizing thermal bonding to another pc wafer. these thermal bonds do not yield up to an applied force equivalent to 150 psi. aqueous fluid transport inside the plastic ce devices was enhanced by uv irradiation treatment of the hydrophobic polycarbonate plastic surfaces prior to thermal bonding. in comparison to glass microchannels, ...	2001	11569809
promoter characterization and genomic organization of the human breast cancer resistance protein (atp-binding cassette transporter g2) gene.	the breast cancer resistance protein (bcrp) gene, formally known as atp-binding cassette transporter g2 (abcg2) gene, encodes an abc half transporter that causes resistance to certain cancer chemotherapeutic drugs when transfected and expressed in drug sensitive cancer cells. here we report the organization of the bcrp gene, and the initial characterization of the bcrp promoter. we identified the genomic sequence of bcrp and its promoter by screening a human genomic lambda phage library, as well ...	2001	11566359
[colony and phage-plaque direct sequencings by dye-terminator methods].	direct sequencing using lambda phage dna and e. coli colonies with plasmid dna is a very powerful technique. almost all of the reported direct sequencing methods involve either radioactive sequencing or fluorescent dye-primer sequencing. we present a direct colony sequencing strategy that uses a dye terminator (bigdye terminator kit) together with dye primer sequencing. we found that single-colony sequencing with the terminator yielded about 500 base pairs of sequence information. signal strengt ...	2001	11558155
para-aminobenzoic acid inhibits a set of sos functions in escherichia coli k12.	paba - vitamin h1 of group b, has obtained increasing fundamental interest as a very potent natural antimutagen after a series of our publications since 1979. in the first set of our experiments, we studied paba in the assays with the alkylating agent n-methyl-n-nitrosourea (mnu). mutagenic efficiency of this agent was suppressed up to 10-fold when paba was administered into escherichia coli cells concurrently with the mutagen or prior to the mutagenic treatment. nmr spectrometric and uv-spectro ...	2001	11551484
phages of dairy bacteria.	bacteriophages of lactic acid bacteria are a threat to industrial milk fermentation. owing to their economical importance, dairy phages became the most thoroughly sequenced phage group in the database. comparative genomics identified related cos-site and pac-site phages, respectively, in lactococci, lactic streptococci and lactobacilli. each group was represented with closely related temperate and virulent phages. over the structural genes their gene maps resembled that of lambdoid coliphages, s ...	2001	11544357
forebrain and midbrain development requires epiblast-restricted otx2 translational control mediated by its 3' utr.	otx genes play an important role in brain development. previous mouse models suggested that the untranslated regions (utrs) of otx2 mrna may contain regulatory element(s) required for its post-transcriptional control in epiblast and neuroectoderm. in order to study this, we have perturbed the 3' utr of otx2 by inserting a small fragment of dna from the lambda phage. otx2(lambda) mutants exhibited proper gastrulation and normal patterning of the early anterior neural plate, but from 8.5 days post ...	2001	11532921
a chimeric activator of transcription that uses two dna-binding domains to make simultaneous contact with pairs of recognition sites.	many well-known transcriptional regulatory proteins are composed of at least two independently folding domains and, typically, only one of these is a dna-binding domain. however, some transcriptional regulators have been described that have more than one dna-binding domain. regulators with a single dna-binding domain often bind co-operatively to the dna in homotypic or heterotypic combinations, and two or more dna-binding domains of a single regulatory protein can also bind co-operatively to sui ...	2001	11532151
an ancient player unmasked: t4 ri encodes a t-specific antiholin.	phage t4 effects lysis by its holin t and its endolysin e. lysis is inhibited (lin) if the infected cell is subjected to secondary infections by t4 phage particles. the t4 ri gene is required for lin in all hosts tested. here, we show that a cloned ri gene can impose a t-specific lin on t-mediated lysis in the context of the phage lambda infective cycle, in the absence of other t4 genes and without secondary infection by t4. moreover, it is shown that the t holin accumulates in the membrane duri ...	2001	11532126
detection of legionellae in hospital water samples by quantitative real-time lightcycler pcr.	contamination of hospital water systems with legionellae is a well-known cause of nosocomial legionellosis. we describe a new real-time lightcycler pcr assay for quantitative determination of legionellae in potable water samples. primers that amplify both a 386-bp fragment of the 16s rrna gene from legionella spp. and a specifically cloned fragment of the phage lambda, added to each sample as an internal inhibitor control, were used. the amplified products were detected by use of a dual-color hy ...	2001	11525995
nucleotide sequence of coliphage hk620 and the evolution of lambdoid phages.	hk620 is a temperate lambdoid bacteriophage that adsorbs to the o-antigen of its host, escherichia coli h. the genome of a temperature-sensitive clear-plaque mutant consists of 38,297 nucleotides in which we recognize 60 open reading frames (orfs). eighteen of these lie in a region of the genome that we call the virion structure domain. the other 42 orfs lie in what we call the metabolic domain. virions of hk620 resemble those of phage p22. the virion structural orfs encode three kinds of putati ...	2001	11518522
elimination of transcriptional interference between tandem genes in plant cells.	plant cells are commonly transformed with two or more tandemly arranged genes, but how orientation affects their expression is not well understood. we investigated the amount of transcriptional interference occurring between two adjacent genes by cloning luciferase and green fluorescent protein (gfp) genes (promoter--coding sequence--terminator) in all possible orientations and expressing the genes in tobacco protoplasts. when two genes are oriented head-to-tail (-->-->), the expression of the d ...	2001	11515369
distinct binding specificity of the multiple pdz domains of inadl, a human protein with homology to inad from drosophila melanogaster.	pdz domains are protein-protein interaction modules that typically bind to short peptide sequences at the carboxyl terminus of target proteins. proteins containing multiple pdz domains often bind to different trans-membrane and intracellular proteins, playing a central role as organizers of multimeric complexes. to characterize the rules underlying the binding specificity of different pdz domains, we have assembled a novel repertoire of random peptides that are displayed at high density at the c ...	2001	11509564
the tgv transgenic vectors for single-copy gene expression from the escherichia coli chromosome.	plasmid-based cloning and expression of genes in escherichia coli can have several problems: plasmid destabilization; toxicity of gene products; inability to achieve complete repression of gene expression; non-physiological overexpression of the cloned gene; titration of regulatory proteins; and the requirement for antibiotic selection. we describe a simple system for cloning and expression of genes in single copy in the e. coli chromosome, using a non-antibiotic selection for transgene insertio ...	2001	11483365
bacteriophage lambda dna packaging: dna site requirements for termination and processivity.	bacteriophage lambda chromosomes are processively packaged into preformed shells, using end-to-end multimers of intracellular viral dna as the packaging substate. a 200 bp long dna segment, cos, contains all the sequences needed for dna packaging. the work reported here shows that efficient dna packaging termination requires cos's i2 segment, in addition to the required termination subsite, cosq, and the nicking site, cosn. efficient processivity requires cosb, in addition to cosq and cosn. an i ...	2001	11478856
viral haemorrhagic septicaemia virus induces vig-2, a new interferon-responsive gene in rainbow trout.	an mrna differential display methodology was used to study the rainbow trout response to viral infection. a new transcript (vig-2) induced by viral haemorrhagic septicaemia virus (vhsv) in rainbow trout leucocytes was identified from the head-kidney. vig-2 was also induced in vivo during experimental infection and following dna immunisation with a plasmid containing a gene encoding the viral glycoprotein. viral induction of vig-2 was blocked by cycloheximide (chx), indicating its dependency on a ...	2001	11478515
cell toxicity caused by products of the p(l) operon of bacteriophage lambda.	induction of a lambda prophage causes the death of the host cell even in the absence of phage replication and lytic functions due to expression of functions from the lambda p(l) operon. we genetically modified the lambda prophage to determine which lambda p(l) operon functions were involved in cell killing. viability assays and flow cytometry were used to monitor cell death and filamentation. the kil gene was shown to cause cell death and filamentation as described previously. another killing ac ...	2001	11470529
identification of the high affinity mn2+ binding site of bacteriophage lambda phosphoprotein phosphatase: effects of metal ligand mutations on electron paramagnetic resonance spectra and phosphatase activities.	bacteriophage lambda phosphoprotein phosphatase (lambdapp) has structural similarity to the mammalian ser/thr phosphoprotein phosphatases (ppps) including the immunosuppressant drug target calcineurin. ppps possess a conserved active site containing a dinuclear metal cluster, with metal ligands provided by a phosphoesterase motif plus two additional histidine residues at the c-terminus. multiple sequence alignment of lambdapp with 28 eubacterial and archeal phosphoesterases identified active sit ...	2001	11467953
single-strand interruptions in replicating chromosomes cause double-strand breaks.	replication-dependent chromosomal breakage suggests that replication forks occasionally run into nicks in template dna and collapse, generating double-strand ends. to model replication fork collapse in vivo, i constructed phage lambda chromosomes carrying the nicking site of m13 bacteriophage and infected with these substrates escherichia coli cells, producing m13 nicking enzyme. i detected double-strand breaks at the nicking sites in lambda dna purified from these cells. the double-strand break ...	2001	11459959
regulation of microcin c51 operon expression: the role of global regulators of transcription.	expression of the microcin c51 operon in escherichia coli cells is regulated as a function of the phase of growth; it is stimulated during the decelerating phase of growth. using single-copy p(mcc)-lac transcriptional fusion (the promoter region of the microcin c51 operon fused to a promoterless lac operon in lambda phage), we showed that transcription from the microcin operon promoter is dependent on sigma(s) (rpos) factor. however, some level of p(mcc)-lac expression is possible in rpos null m ...	2001	11446515
what makes the bacteriophage lambda red system useful for genetic engineering: molecular mechanism and biological function.	recent studies have generated interest in the use of the homologous recombination system of bacteriophage lambda for genetic engineering. the system, called red, consists primarily of three proteins: lambda exonuclease, which processively digests the 5'-ended strand of a dsdna end; beta protein, which binds to ssdna and promotes strand annealing; and gamma protein, which binds to the bacterial recbcd enzyme and inhibits its activities. these proteins induce a 'hyper-rec' state in escherichia col ...	2001	11445160
seqa, the escherichia coli origin sequestration protein, is also a specific transcription factor.	the seqa protein is a negative regulator of initiation of dna replication in the escherichia coli chromosome. here, we demonstrate that seqa stimulates transcription from the bacteriophage lambda pr promoter both in vivo and in vitro. the activity of the lambda pl promoter was found not to be affected by this protein. seqa-mediated stimulation of pr was dependent on the state of template methylation: transcription was activated on fully methylated and hemimethylated templates but not on an unmet ...	2001	11442835
bacteriophage lambda-based expression vectors.	bacteriophage lambda has been in use as a cloning vector for over 25 years, and has been used extensively as an expression vector. the efficiency of packaging and infection, and the simplicity of plaque screening are advantages of lambda as a cloning vector. a number of ingenious modifications help overcome the disadvantages associated with its mode of growth and its size. some lambda vectors have been designed to be readily converted into plasmids or phagemids, and there are a variety of promot ...	2001	11434310
a plasmid cloning vector with precisely regulatable copy number in escherichia coli.	we have developed a genetic system allowing for precise regulation of plasmid copy number in escherichia coli cells. a cloning vector based on this system is described in this article. the ptc lambda 3 plasmid is a lambda replicon, but transcription controlling initiation of plasmid dna replication starts from the pteta promoter instead of phage lambda pr promoter. additionally, activity of pteta promoter is negatively controlled by the tetr repressor whose gene is located on the same plasmid ve ...	2001	11434307
the double mechanism of incompatibility between lambda plasmids and escherichia coli dnaa(ts) host cells.	for plasmids derived from bacteriophage lambda, the initiation of bidirectional dna replication from orilambda depends on the stimulation of transcription from the p(r) promoter by the host replication initiator protein dnaa. certain escherichia coli dnaa(ts) mutants cannot be transformed by wild-type lambda plasmids even at the temperature permissive to cell growth. this plasmid-host incompatibility appeared to be due to inefficient stimulation of transcription from the p(r) promoter by the mut ...	2001	11429468
specific and non-specific interactions of integration host factor with dna: thermodynamic evidence for disruption of multiple ihf surface salt-bridges coupled to dna binding.	site-specific dna binding of architectural protein integration host factor (ihf) is involved in formation of functional multiprotein-dna assemblies in escherichia coli, while non-specific binding of ihf and other histone-like proteins serves to structure the nucleoid. here, we report an isothermal titration calorimetry study of the thermodynamics of binding ihf to a 34 bp fragment composed entirely of the specific h' site from lambda-phage dna. at low to moderate [k(+)] (60-100 mm), strong compe ...	2001	11428896
unfolding individual nucleosomes by stretching single chromatin fibers with optical tweezers.	single chromatin fibers were assembled directly in the flow cell of an optical tweezers setup. a single lambda phage dna molecule, suspended between two polystyrene beads, was exposed to a xenopus laevis egg extract, leading to chromatin assembly with concomitant apparent shortening of the dna molecule. assembly was force-dependent and could not take place at forces exceeding 10 pn. the assembled single chromatin fiber was subjected to stretching by controlled movement of one of the beads with t ...	2001	11427891
a small protein-protein interaction domain common to klcb and global regulators kora and trba of promiscuous incp plasmids.	the kor regulon of broad host-range, incompatibility group p (incp) plasmids uses the kora, korb, and korc repressors to regulate expression of genes for replication, conjugation, segregation, and host range. one operon, kilc, encodes the korc repressor and two genes of unknown function (klca and klcb). the predicted sequences of the 51.1 kda klcb protein, the 11.3 kda kora repressor, and another small (13.5 kda) regulatory protein, trba, show a highly related 35 amino acid residue segment (v-l- ...	2001	11419936
structure of the hodgkin's lymphoma-associated human cd30 gene and the influence of a microsatellite region on its expression in cd30(+) cell lines.	the cd30 antigen is a member of the tumor necrosis factor receptor (tnfr) family which is overexpressed on the surface of the tumor cells of hodgkin's lymphoma, anaplastic large cell lymphoma (alcl), and embryonal carcinoma of the testis. in this study the entire cd30 gene which is more than 24000 bp long and organized in eight exons was characterized by analyzing cosmid and phage lambda clones from human placental libraries with long-range polymerase chain reaction (pcr) and sequencing. differe ...	2001	11418184
variable range hopping and electrical conductivity along the dna double helix.	we present a model to describe electrical conductivity along the dna double helix. in this model, dna is considered as a one-dimensional disordered system, and electrons are transported via variable range hopping between localized states. thermal structural fluctuations in dna further localize electronic wave functions, giving rise to a temperature-dependent localization length. the model quantitatively explains the temperature dependence of the conductivity observed in the lambda phage dna (lam ...	2001	11415418
efficient transformation of filamentous fungus pleurotus ostreatus using single-strand carrier dna.	the effects of carrier dnas on the transformation of the basidiomycete pleurotus ostreatus were analyzed. when lambda phage dna was added to a transformation mixture containing protoplasts and cbxr vector plasmid, an increased number of drug-resistant transformants was observed on a screening plate containing 2 microg carboxin/ml. the highest efficiency (about 200 transformants/microg vector plasmid) was obtained by the addition of heat-denatured lambda dna, which gave yields approximately 50-fo ...	2001	11414321
defining cosq, the site required for termination of bacteriophage lambda dna packaging.	bacteriophage lambda is a double-stranded dna virus that processes concatemeric dna into virion chromosomes by cutting at specific recognition sites termed cos. a cos is composed of three subsites: cosn, the nicking site; cosb, required for packaging initiation; and cosq, required for termination of chromosome packaging. during packaging termination, nicking of the bottom strand of cosn depends on cosq, suggesting that cosq is needed to deliver terminase to the bottom strand of cosn to carry out ...	2001	11404316
repression of transcription initiation at 434 p(r) by 434 repressor: effects on transition of a closed to an open promoter complex.	the lambdoid bacteriophage repressors function both as transcription activators and repressors. regulation of transcription at the adjacent, but divergent promoters, p(rm) and p(r), determines the phage's choice between the lytic and lysogenic development pathways. here, we demonstrate that 434 repressor bound at 434 o(r)1 alone is not sufficient to repress transcription from 434 p(r,) but that 434 repressor bound at 434 o(r)2 alone is necessary and sufficient to repress p(r )transcription. this ...	2001	11397081
expression of unphosphorylated form of human double-stranded rna-activated protein kinase in escherichia coli.	interferon (ifn)-inducible, double-stranded (dsrna)-activated protein kinase (pkr) is a key mediator of the antiviral and antiproliferative effects of ifn. pkr is present within cells in a latent state. in response to binding dsrna, the enzyme becomes activated, causing autophosphorylation and an increase in specific kinase activity. in order to study pkr and its inhibitors, a large amount of the enzyme in its latent, unphosphorylated state is required. when pkr is fused to glutathione s-transfe ...	2001	11396973
neural model of the genetic network.	many cell control processes consist of networks of interacting elements that affect the state of each other over time. such an arrangement resembles the principles of artificial neural networks, in which the state of a particular node depends on the combination of the states of other neurons. the lambda bacteriophage lysis/lysogeny decision circuit can be represented by such a network. it is used here as a model for testing the validity of a neural approach to the analysis of genetic networks. t ...	2001	11395518
activities of vire1 and the vire1 secretion chaperone in export of the multifunctional vire2 effector via an agrobacterium type iv secretion pathway.	agrobacterium tumefaciens uses a type iv secretion system to deliver oncogenic nucleoprotein particles and effector proteins, such as the multifunctional vire2 protein, to plant cells. in this study, we examined the function of vire1 and its product, the vire1 secretion chaperone, in mediating vire2 export. a nonpolar vire1 null mutant accumulated low levels of vire2, and trans expression of vire1 in this mutant only partially restored vire2 abundance. deletion of vire1 did not affect transcript ...	2001	11395448
high efficiency mutagenesis, repair, and engineering of chromosomal dna using single-stranded oligonucleotides.	homologous dna recombination is a fundamental, regenerative process within living organisms. however, in most organisms, homologous recombination is a rare event, requiring a complex set of reactions and extensive homology. we demonstrate in this paper that beta protein of phage lambda generates recombinants in chromosomal dna by using synthetic single-stranded dnas (ssdna) as short as 30 bases long. this ssdna recombination can be used to mutagenize or repair the chromosome with efficiencies th ...	2001	11381128
chromosomal location of murine disabled-2 gene and structural comparison with its human ortholog.	disabled-2 (dab2) is one of the two mammalian orthologs of the drosophila disabled. the three spliced forms, p96, p93, and p67 of murine dab2 cdnas were first isolated as phosphoproteins functioning in the macrophage csf-1 signal transduction pathway. subsequently, the involvement of dab2 in ovarian cancer development has been investigated: dab2 expression is lost or greatly diminished in breast and ovarian cancers, and gene deletions have been found. regulation of disabled-2 expression is also ...	2001	11368898
two novel pao-like retrotransposons (kamikaze and yamato) from the silkworm species bombyx mori and b. mandarina: common structural features of pao-like elements.	to characterize the structural features common to pao-like retrotransposons, we analyzed two lambda phage clones which contain the pao-like elements from the silkworm species bombyx mori and b. mandarinia, and copies of pao itself and ninja of drosophila simulans, amplified by pcr. we previously identified two randomly amplified polymorphic dnas (rapds), w-kamikaze and w-yamato, from b. mori and b. mandarina, which are part of two novel pao-like retrotransposons, kamikaze and yamato, respectivel ...	2001	11361350
functional analysis of the phage t4 holin in a lambda context.	phage lambda hybrids were constructed by inserting the t gene of phage t4 in place of the lambda holin gene, s. induction of the hybrid phage resulted in lysis that was just as abrupt as, but occurred much earlier in the vegetative cycle than, that obtained with lambda, indicating that t is indeed a holin gene. moreover, it was possible to impose lysis inhibition (lin) on induction of the hybrid phage, but not of the parental lambda phage, by superinfection with lin-competent t4. the imposition ...	2001	11361346
cloning and expression analysis of nhl1, a gene encoding an extracellular lipase from the fungal pea pathogen nectria haematococca mp vi (fusarium solani f. sp. pisi) that is expressed in planta.	the filamentous fungus nectria haematococca (anamorph fusarium solani f. sp. pisi) resides in soil, and attacks pea seedlings in the area of the underground epicotyl and upper tap root, causing foot rot disease. we detected lipase activity during in vitro growth of n. haematococca. subsequently, a lipase gene was cloned and functionally characterised by heterologous expression in saccharomyces cerevisiae. the full-length cdna of 1152 bp was cloned using a 3' race-pcr approach coupled with cdna l ...	2001	11361331
facilitation of bacteriophage lambda dna injection by inner membrane proteins of the bacterial phosphoenol-pyruvate: carbohydrate phosphotransferase system (pts).	infection of escherichia coli by bacteriophage lambda depends on two membrane protein complexes: (i) maltoporin (lamb) in the outer membrane for adsorption and (ii) the iic(man)-iid(man) complex of the mannose transporter in the inner membrane for dna penetration. iic(man) and iid(man) are components of the phosphoenolpyruvate: sugar phosphotransferase system (pts) which together with the iiab(man) subunit mediate transport and phosphorylation of sugars. to identify structural determinants impor ...	2001	11361066
molecular nature of ultraviolet b light-induced deletions in the murine epidermis.	depletion of the stratospheric ozone layer leads to an increase in ambient uv loads, which are expected to raise skin cancer incidences. tumor development in the skin could be a multistep process in which various genetic alterations, such as point mutations and deletions, occur successively. here, we demonstrate that uvb irradiation efficiently induces deletions in the epidermis using a novel transgenic mouse, gpt delta. in this mouse model, deletions in lambda dna integrated in the chromosome a ...	2001	11358805
[changes in rigidity of the polymeric chain of the lambda-phage dna in aqueous solutions with low ionic strength over the ph range 4-9.5].	it was shown that the decrease in the rigidity (persistent length) of phage lambda dna, revealed previously by laser correlation spectroscopy, occurs in an aqueous solution at concentrations of sodium salts less than 10(-2) m in the ph range 4-9.5. dna coils of anomalously small size (approximately twofold less than the size reported by other authors) are formed. the formation of these coils is likely to be due to the separation of "normal", i.e., rigid dna coils into two phases, which occurs as ...	2001	11357334
the structure of the coliphage hk022 nun protein-lambda-phage boxb rna complex. implications for the mechanism of transcription termination.	nun protein from coliphage hk022 binds to phage boxb rna and functions, in contrast to phage lambda n protein, as a transcriptional terminator. the basic nun-(10-44) peptide contains the boxb rna binding arginine rich motif, arm. the peptide binds boxb rna and competes with the phage lambda arm peptide n-(1-36) as indicated by nuclear magnetic resonance (nmr) spectroscopy titrations. in two-dimensional nuclear overhauser enhancement spectroscopy experiments boxb rna in complex with nun-(20-44) e ...	2001	11356847
maldi-tof mass spectrometric method for detection of hybridized dna oligomers.	two new approaches for nucleic acid hybridizations by maldi-tof mass spectrometry are described. hybridization using genomic dna without polymerase chain reaction was demonstrated. total genomic dna of bacteriophages bound to charge-modified nylon membranes was identified by the hybridization of species-specific oligonucleotide probes. lambda-phage dna and m13 were used for the test with good success. since maldi-tof mass spectrometry can be used to measure the molecular weights of different pro ...	2001	11354500
protein transduction domain of hiv-1 tat protein promotes efficient delivery of dna into mammalian cells.	the plasma membrane of mammalian cells is one of the tight barriers against gene transfer by synthetic delivery systems. various agents have been used to facilitate gene transfer by destabilizing the endosomal membrane under acidic conditions, but their utility is limited, especially for gene transfer in vivo. in this article, we report that the protein transduction domain of human immunodeficiency virus type 1 tat protein (tat peptide) greatly facilitates gene transfer via membrane destabilizat ...	2001	11346640
unusual evolutionary history of the trna splicing endonuclease enda: relationship to the laglidadg and pd-(d/e)xk deoxyribonucleases.	the trna splicing endoribonuclease enda from methanococcus jannaschii is a homotetramer formed via heterologous interaction between the two pairs of homodimers. each monomer consists of two alpha/beta domains, the n-terminal domain (ntd) and the c-terminal domain (ctd) containing the rnase a-like active site. comparison of the enda coordinates with the publicly available protein structure database revealed the similarity of both domains to site-specific deoxyribonucleases: the ntd to the laglida ...	2001	11344334
crystal structure of the lytic transglycosylase from bacteriophage lambda in complex with hexa-n-acetylchitohexaose.	the three-dimensional structure of the lytic transglycosylase from bacteriophage lambda, also known as bacteriophage lambda lysozyme, complexed to the hexasaccharide inhibitor, hexa-n-acetylchitohexaose, has been determined by x-ray crystallography at 2.6 a resolution. the unit cell contains two molecules of the lytic transglycosylase with two hexasaccharides bound. each enzyme molecule is found to interact with four n-acetylglucosamine units from one hexasaccharide (subsites a-d) and two n-acet ...	2001	11341831
a structural view of cre-loxp site-specific recombination.	structural models of site-specific recombinases from the lambda integrase family of enzymes have in the last four years provided an important new perspective on the three-dimensional nature of the recombination pathway. members of this family, which include the bacteriophage p1 cre recombinase, bacteriophage lambda integrase, the yeast flp recombinase, and the bacterial xercd recombinases, exchange strands between dna substrates in a stepwise process. one pair of strands is exchanged to form a h ...	2001	11340053
cloning, expression, and characterization of a family 52 beta-xylosidase gene (xysb) of a multiple-xylanase-producing bacterium, aeromonas caviae me-1.	a lambda phage genomic library of aeromonas caviae me-1, a multiple-xylanase-producing bacterium, was screened for xylan degradation activities. we isolated one clone, b65, which had weak xylanase activity, by the dns method, but gave no visible bands on zymogram assay using sds-xylan-page. based on tlc analyses of enzymatic products and some glycosidase assays using p-nitrophenyl substrates, we established that pb65 encodes a beta-xylosidase gene. in the nucleotide sequence analysis, we found a ...	2001	11330658
the herpesvirus alkaline exonuclease belongs to the restriction endonuclease pd-(d/e)xk superfamily: insight from molecular modeling and phylogenetic analysis.	the pd-(d/e)xk superfamily of deoxyribonucleases (enases) comprises restriction endonucleases, exonucleases and nicking enzymes, which share a common fold and the architecture of the active site. their extreme divergence generally hampers identification of novel members based solely on sequence comparisons. here we report a remote similarity between the phage lambda exonuclease (lambda-exo), branching out early in the evolutionary history of enases (3), with the family of alkaline exonucleases ( ...	2001	11324759
bacteriophage lambda ciii gene product has an additional function apart from inhibition of cii degradation.	for lysogenization of escherichia coli cells by bacteriophage lambda, functions of three lambda genes called c are necessary. the ci gene codes for a repressor that blocks activities of lytic promoters. however, early after infection, expression of ci is dependent on the function of the cii gene, coding for a specific transcriptional activator. the cii protein is unstable in e. coli cells due to ftsh-mediated proteolysis. the ciii gene product is an inhibitor of the ftsh protease. here we demons ...	2001	11324748
sequence analysis of insecticidal genes from xenorhabdus nematophilus pmfi296.	three strains of xenorhabdus nematophilus showed insecticidal activity when fed to pieris brassicae (cabbage white butterfly) larvae. from one of these strains (x. nematophilus pmfi296) a cosmid genome library was prepared in escherichia coli and screened for oral insecticidal activity. two overlapping cosmid clones were shown to encode insecticidal proteins, which had activity when expressed in e. coli (50% lethal concentration [lc(50)] of 2 to 6 microg of total protein/g of diet). the complete ...	2001	11319082
elevated mutant frequencies and increased c : g-->t : a transitions in mlh1-/- versus pms2-/- murine small intestinal epithelial cells.	mutations in dna mismatch repair (mmr) genes are associated with increased genomic instability and susceptibility to cancer. mice rendered deficient in either mlh1 or pms2 as a result of gene targeting are prone to tumorigenesis, particularly, lymphomas. in addition, although mlh1-/- mice also develop small intestinal adenomas and adenocarcinomas, pms2-/- animals remain free of such tumors. to establish whether this phenotypic dichotomy might be associated with a quantitative and/or qualitative ...	2001	11313994
the solution structure of bacteriophage lambda protein w, a small morphogenetic protein possessing a novel fold.	protein w (gpw) from bacteriophage lambda is required for the stabilization of dna within the phage head and for attachment of tails onto the head during morphogenesis. although comprised of only 68 residues, it likely interacts with at least two other proteins in the mature phage and with dna. thus, gpw is an intriguing subject for detailed structural studies. we have determined its solution structure using nmr spectroscopy and have found it to possesses a novel fold consisting of two alpha-hel ...	2001	11302702
selection of ligands by panning of domain libraries displayed on phage lambda reveals new potential partners of synaptojanin 1.	one of the goals of functional genomics is the description of reliable and complete protein interaction networks. to facilitate ligand discovery from complex protein mixtures, we have developed an improved approach that is affected by a negligible fraction of false positives. we have combined a novel technique based on the display of cdna libraries on the capsid of bacteriophage lambda and an efficient plaque assay to reveal phage displaying ligands that are enriched after only a couple of affin ...	2001	11292345
inheritance of the replication complex: a unique or common phenomenon in the control of dna replication?	early models of the regulation of initiation of dna replication by protein complexes predicted that binding of a replication initiator protein to a replicator region is required for initiation of each dna replication round, since after the initiation event the replication initiator should dissociate from dna. it was, therefore, assumed that binding of the replication initiator is a signal for triggering dna replication. however, more recent investigations have revealed that in many replicons thi ...	2001	11285745
bacteriophage lambda: alive and well and still doing its thing.	the lambda (lambda) family of bacteriophages continues to provide significant insights into the understanding of basic biological processes, as well as useful technological innovations. areas in which recent advances have occurred include transcription elongation, repressor interactions, genomics and post-transcriptional regulation. the homologous lambda recombination functions have been exploited as an efficient in vivo recombinant engineering system for functional genomic studies. the virulenc ...	2001	11282477
biophysical characterization of the dna binding domain of gpnu1, a viral dna packaging protein.	terminase enzymes are common to double-stranded dna viruses. these enzymes "package" the viral genome into a pre-formed capsid. terminase from bacteriophage lambda is composed of gpa (72.4 kda) and gpnu1 (20.4 kda) subunits. we have described the expression and biochemical characterization of gpnu1deltak100, a construct comprising the n-terminal 100 amino acids of gpnu1 (yang, q., de beer, t., woods, l., meyer, j., manning, m., overduin, m., and catalano, c. e. (1999) biochemistry 38, 465-477). ...	2001	11279084
revisiting the lysogenization control of bacteriophage lambda. identification and characterization of a new host component, hfld.	upon infection to the escherichia coli cell, the genome of bacteriophage lambda either replicates to form new progenies (lytic growth) or integrates into the host chromosome (lysogenization). the lambda cii protein is a key determinant in the lysis-lysogeny decision. it is a short-lived transcription activator for the lambda genes essential for lysogeny establishment. in this study, we isolated a new class of hfl (high frequency lysogenization) mutants of e. coli, using a new selection for enhan ...	2001	11278968
foreign dna integration. genome-wide perturbations of methylation and transcription in the recipient genomes.	in hamster cells transgenic for the dna of adenovirus type 12 (ad12) or for the dna of bacteriophage lambda, the patterns of dna methylation in specific cellular genes or dna segments remote from the site of transgene insertion were altered. in the present report, a wide scope of cellular dna segments and genes was analyzed. the technique of methylation-sensitive representational difference analysis (ms-rda) was based on a subtractive hybridization protocol after selecting against dna segments t ...	2001	11278495
complete structural characterisation of the mammalian and drosophila traf genes: implications for traf evolution and the role of ring finger splice variants.	the complete murine traf2 gene was obtained using a lambda phage and pcr cloning strategy. the gene was found to consist of ten coding and one 5' non-coding exon spread over 28 kbp of dna. we also report the basic structure of the human traf5 and traf6 genes obtained by analysis of the genomic dna database. comparison of these three gene structures, along with those previously described for traf1, traf3 and traf4, revealed the evolutionary relationship between the six known mammalian trafs. the ...	2000	11275257
methylation by a mutant t2 dna [n(6)-adenine] methyltransferase expands the usage of reca-assisted endonuclease (rare) cleavage.	properties of a mutant bacteriophage t2 dna [n:(6)-adenine] methyltransferase (t2 dam mtase) have been investigated for its potential utilization in reca-assisted restriction endonuclease (rare) cleavage. steady-state kinetic analyses with oligonucleotide duplexes revealed that, compared to wild-type t4 dam, both wild-type t2 dam and mutant t2 dam p126s had a 1.5-fold higher k(cat) in methylating canonical gatc sites. additionally, t2 dam p126s showed increased efficiencies in methylation of non ...	2001	11266550
hepatitis b virus x protein acts as a tumor promoter in development of diethylnitrosamine-induced preneoplastic lesions.	chronic infection with hepatitis b virus (hbv) is one of the major etiological factors in the development of human hepatocellular carcinoma. transgenic mice that express the hbv x protein (hbx) have previously been shown to be more sensitive to the effects of hepatocarcinogens. although the mechanism for this cofactor role remains unknown, the ability of hbx to inhibit dna repair and to influence cell cycle progression suggests two possible pathways. to investigate these possibilities in vivo, w ...	2001	11264374
polymerase chain reaction in polymeric microchips: dna amplification in less than 240 seconds.	there is much interest in developing methods amenable to amplifying nucleic acids by the polymerase chain reaction (pcr) in small volumes in microfabricated devices. the use of infrared-mediated temperature control to accurately thermocycle microliter volumes in microchips fabricated from polyimide is demonstrated. amplification of a 500-base-pair fragment of lambda-phage dna was achieved in a 1.7-microl chamber containing a thermocouple that allowed for accurate control of temperature. while pr ...	2001	11262165
dominant-negative mutants of prgx: evidence for a role for prgx dimerization in negative regulation of pheromone-inducible conjugation.	prgx negatively regulates prgq transcriptional readthrough in the pheromone-inducible enterococcal conjugative plasmid pcf10. we isolated and characterized 13 dominant-negative prgx mutants, all of which mapped in either the n- or the c-terminus of prgx. in all mutants, the in vivo level of qa rna, an antisense rna to prgq rna, was greatly reduced. when oligomerization of prgx was tested with a phage lambda ci repressor fusion system, the oligomerization domain was found to be between amino acid ...	2001	11251846
papain does not cleave operator-bound lambda repressor: structural characterization of the carboxy terminal domain and the hinge.	the circular dichroism spectra of three different purified carboxy terminal fragments 93-236, 112-236 and 132-236 of the bacteriophage lambda ci repressor have been measured and compared with those of the intact repressor and the amino terminal fragment 1-92. all three carboxy terminal fragments contain mostly beta-strands and loops, a minor helix content increasing with the size of the fragment, showing that the 93-131 region previously called a hinge is structured. fourier transformed infrared ...	2001	11245251
selection of rna-binding peptides using mrna-peptide fusions.	we have been working to apply in vitro selection to isolate novel rna-binding peptides. to do this, we use mrna-protein fusions, peptides covalently attached to their own mrna. here, we report selection protocols developed using the arginine-rich domain of bacteriophage lambda-n protein and its binding target, the boxb rna. systematic investigation of possible paths for a selection round has allowed us to design a reliable and efficient protocol to enrich rna-binding peptides from nonfunctional ...	2001	11243841
regulation of the switch from early to late bacteriophage lambda dna replication.	there are two modes of bacteriophage lambda dna replication following infection of its host, escherichia coli. early after infection, replication occurs according to the theta (theta or circle-to-circle) mode, and is later switched to the sigma (sigma or rolling-circle) mode. it is not known how this switch, occurring at a specific time in the infection cycle, is regulated. here it is demonstrated that in wild-type cells the replication starting from orilambda proceeds both bidirectionally and u ...	2001	11238961
the neurospora crassa genome: cosmid libraries sorted by chromosome.	a neurospora crassa cosmid library of 12,000 clones (at least nine genome equivalents) has been created using an improved cosmid vector plorist6xh, which contains a bacteriophage lambda origin of replication for low-copy-number replication in bacteria and the hygromycin phosphotransferase marker for direct selection in fungi. the electrophoretic karyotype of the seven chromosomes comprising the 42.9-mb n. crassa genome was resolved using two translocation strains. using gel-purified chromosomal ...	2001	11238388
initiation of a sarcocystis neurona expressed sequence tag (est) sequencing project: a preliminary report.	to accelerate genetic and molecular characterization of sarcocystis neurona, the primary causative agent of equine protozoal myeloencephalitis (epm), a sequencing project has been initiated that will generate approximately 7000-8000 expressed sequence tags (ests) from this apicomplexan parasite. poly(a)(+) rna was isolated from culture-derived s. neurona merozoites, and a cdna library was constructed in a unidirectional lambda phage cloning vector. sixty phage clones were randomly picked from th ...	2001	11223203
occurrence and characterization of escherichia coli o157 isolated from cattle in norway.	faecal samples from 504 imported beef cattle were screened to investigate the occurrence of escherichia coli o157. the results were compared with those from a previous screening of norwegian dairy cattle, and the occurrence was found to be higher in the imported beef cattle. the e. coli o157 isolates from the previous and present studies were characterized for the genes encoding for shigatoxin 1 (stx1), shigatoxin 2 (stx2), the intimin protein (eae) and the flagellar protein h7 (flic) using pcr ...	2001	11214668